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Barroux M, Horstmann J, Fricke L, Schömig L, Werner M, Kraynova E, Kamarádová K, Fléjou JF, Maerkel B, Kumarasinghe MP, Vieth M, Westerhoff M, Patil DT, Steiger K, Becker KF, Weichert W, Schmid RM, Quante M, Slotta-Huspenina J. Histological evaluation of PAXgene tissue fixation in Barrett’s esophagus and esophageal adenocarcinoma diagnostics. Virchows Arch 2022; 482:887-898. [PMID: 36527466 PMCID: PMC10156762 DOI: 10.1007/s00428-022-03471-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 11/01/2022] [Accepted: 11/30/2022] [Indexed: 12/23/2022]
Abstract
Abstract
The dysplasia grading of Barrett’s esophagus (BE), based on the histomorphological assessment of formalin-fixed, paraffin-embedded (FFPE) tissue, suffers from high interobserver variability leading to an unsatisfactory prediction of cancer risk. Thus, pre-analytic preservation of biological molecules, which could improve risk prediction in BE enabling molecular and genetic analysis, is needed. We aimed to evaluate such a molecular pre-analytic fixation tool, PAXgene-fixed paraffin-embedded (PFPE) biopsies, and their suitability for histomorphological BE diagnostics in comparison to FFPE. In a ring trial, 9 GI pathologists evaluated 116 digital BE slides of non-dysplastic BE (NDBE), low-grade dysplasia (LGD), high-grade dysplasia (HGD), and esophageal adenocarcinomas (EAC) using virtual microscopy. Overall quality, cytological and histomorphological parameters, dysplasia criteria, and diagnosis were analyzed. PFPE showed better preservation of nuclear details as chromatin and nucleoli, whereas overall quality and histomorphologic parameters as visibility of basal lamina, goblet cells, and presence of artifacts were scored as equal to FFPE. The interobserver reproducibility with regard to the diagnosis was best for NDBE and EAC (κF = 0.72–0.75) and poor for LGD and HGD (κF = 0.13–0.3) in both. In conclusion, our data suggest that PFPE allows equally confident histomorphological diagnosis of BE and EAC, introducing a novel tool for molecular analysis and parallel histomorphological evaluation.
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Affiliation(s)
- Melissa Barroux
- Klinikum Rechts Der Isar, Medical Clinic and Polyclinic II, Technical University of Munich, Munich, Germany.
| | - Julia Horstmann
- Klinikum Rechts Der Isar, Medical Clinic and Polyclinic II, Technical University of Munich, Munich, Germany
| | - Lisa Fricke
- Klinikum Rechts Der Isar, Medical Clinic and Polyclinic II, Technical University of Munich, Munich, Germany
| | - Linus Schömig
- Department of Medicine II, Universitaetsklinikum Freiburg, Freiburg, Germany
| | - Martin Werner
- Institute for Surgical Pathology, Medical Center-University of Freiburg and Faculty of Medicine, University of Freiburg, 79106, Freiburg, Germany
| | - Ekaterina Kraynova
- Department of Pathology, Yaroslavl Regional Cancer Hospital, Yaroslavl, Russian Federation
| | - Katerina Kamarádová
- The Fingerland Department of Pathology, Faculty of Medicine and University Hospital, Charles University, Hradec Králové, Czech Republic
| | - Jean-François Fléjou
- Service d'Anatomie Pathologique, AP-HP, Faculté de Médecine Sorbonne, Hôpital Saint-Antoine, Université, 75012, Paris, France
| | - Bruno Maerkel
- Institute of Pathology and Molecular Diagnostics, University Medical Center Augsburg, Augsburg, Germany
| | - M Priyanthi Kumarasinghe
- Department of Pathology, PathWest Laboratory-University of Western Australia, WA, Perth, Australia
| | - Michael Vieth
- Institute for Pathology, Friedrich-Alexander-University Erlangen-Nuremberg, Klinikum Bayreuth, Bayreuth, Germany
| | | | - Deepa T Patil
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, USA
| | - Katja Steiger
- Institute of Pathology, Technical University of Munich, Munich, Germany
| | | | - Wilko Weichert
- Institute of Pathology, Technical University of Munich, Munich, Germany
| | - Roland M Schmid
- Klinikum Rechts Der Isar, Medical Clinic and Polyclinic II, Technical University of Munich, Munich, Germany
| | - Michael Quante
- Klinikum Rechts Der Isar, Medical Clinic and Polyclinic II, Technical University of Munich, Munich, Germany
- Department of Medicine II, Universitaetsklinikum Freiburg, Freiburg, Germany
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2
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Paramasivam P, Stöter M, Corradi E, Dalla Costa I, Höijer A, Bartesaghi S, Sabirsh A, Lindfors L, Yanez Arteta M, Nordberg P, Andersson S, Baudet ML, Bickle M, Zerial M. Quantitative intracellular retention of delivered RNAs through optimized cell fixation and immunostaining. RNA (NEW YORK, N.Y.) 2022; 28:433-446. [PMID: 34949721 PMCID: PMC8848937 DOI: 10.1261/rna.078895.121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 12/12/2021] [Indexed: 06/14/2023]
Abstract
Detection of nucleic acids within subcellular compartments is key to understanding their function. Determining the intracellular distribution of nucleic acids requires quantitative retention and estimation of their association with different organelles by immunofluorescence microscopy. This is particularly important for the delivery of nucleic acid therapeutics, which depends on endocytic uptake and endosomal escape. However, the current protocols fail to preserve the majority of exogenously delivered nucleic acids in the cytoplasm. To solve this problem, by monitoring Cy5-labeled mRNA delivered to primary human adipocytes via lipid nanoparticles (LNP), we optimized cell fixation, permeabilization, and immunostaining of a number of organelle markers, achieving quantitative retention of mRNA and allowing visualization of levels that escape detection using conventional procedures. The optimized protocol proved effective on exogenously delivered siRNA, miRNA, as well as endogenous miRNA. Our protocol is compatible with RNA probes of single molecule fluorescence in situ hybridization (smFISH) and molecular beacon, thus demonstrating that it is broadly applicable to study a variety of nucleic acids in cultured cells.
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Affiliation(s)
- Prasath Paramasivam
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Martin Stöter
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Eloina Corradi
- Department CIBIO, University of Trento, Trento 38123, Italy
| | | | - Andreas Höijer
- Advanced Drug Delivery, Pharmaceutical Science R&D, AstraZeneca, 43150 Gothenburg, Sweden
| | - Stefano Bartesaghi
- Bioscience Metabolism, Research and Early Development Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, 43150 Gothenburg, Sweden
| | - Alan Sabirsh
- Advanced Drug Delivery, Pharmaceutical Science R&D, AstraZeneca, 43150 Gothenburg, Sweden
| | - Lennart Lindfors
- Advanced Drug Delivery, Pharmaceutical Science R&D, AstraZeneca, 43150 Gothenburg, Sweden
| | - Marianna Yanez Arteta
- Advanced Drug Delivery, Pharmaceutical Science R&D, AstraZeneca, 43150 Gothenburg, Sweden
| | - Peter Nordberg
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, 43150 Gothenburg, Sweden
| | - Shalini Andersson
- Oligonucleotide Discovery, Discovery Sciences R&D, AstraZeneca, 43150 Gothenburg, Sweden
| | | | - Marc Bickle
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Marino Zerial
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
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3
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Alternative tissue fixation for combined histopathological and molecular analysis in a clinically representative setting. Histochem Cell Biol 2021; 156:595-607. [PMID: 34905068 PMCID: PMC8695534 DOI: 10.1007/s00418-021-02029-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/31/2021] [Indexed: 11/26/2022]
Abstract
Formalin is the principal tissue fixative used worldwide for clinical and research purposes. Despite optimal preservation of morphology, its preservation of DNA and RNA is poor. As clinical diagnostics increasingly incorporates molecular-based analysis, the requirement for maintaining nucleic acid quality is of increasing importance. Here we assess an alternative non-formalin-based tissue fixation method, PAXgene Tissue system, with the aim of better preserving nucleic acids, while maintaining the quality of the tissue to be used for vital existing diagnostic techniques. In this study, these criteria are assessed in a clinically representative setting. In total, 203 paired PAXgene Tissue and formalin-fixed samples were obtained. Blind-scored haematoxylin and eosin (H&E) sections showed comparable and acceptable staining. Immunohistochemistry (IHC) staining was suboptimal using existing protocols but improved with minor method adjustment and optimisation. Quality of DNA and RNA was significantly improved by PAXgene tissue fixation [RIN 2.8 versus 3.8 (p < 0.01), DIN 5.68 versus 6.77 (p < 0.001)], which translated into improved performance on qPCR assay. These results demonstrate the potential of PAXgene Tissue to be used routinely in place of formalin, maintaining adequate histological staining and significantly improving the preservation of biological molecules in the genomic era.
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4
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Frasquilho SG, Sanchez I, Yoo C, Antunes L, Bellora C, Mathieson W. Do Tissues Fixed in a Non-crosslinking Fixative Require a Dedicated Formalin-free Processor? J Histochem Cytochem 2021; 69:389-405. [PMID: 34010071 DOI: 10.1369/00221554211017859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
We evaluate the consequences of processing alcohol-fixed tissue in a processor previously used for formalin-fixed tissue. Biospecimens fixed in PAXgene Tissue Fixative were cut into three pieces then processed in a flushed tissue processor previously used for formalin-fixed, paraffin-embedded (FFPE) blocks (neutral buffered formalin [NBF]+ve), a formalin-free system (NBF-ve), or left unprocessed. Histomorphology and immunohistochemistry were compared using hematoxylin/eosin staining and antibodies for MLH-1, Ki-67, and CK-7. Nucleic acid was extracted using the PAXgene Tissue RNA/DNA kits and an FFPE RNA extraction kit. RNA integrity was assessed using RNA integrity number (RIN), reverse transcription polymerase chain reaction (RT-PCR) (four amplicons), and quantitative RT-PCR (three genes). For DNA, multiplex PCR, quantitative PCR, DNA integrity number, and gel electrophoresis were used. Compared with NBF-ve, RNA from NBF+ve blocks had 88% lower yield and poorer purity; average RIN reduced from 5.0 to 3.8, amplicon length was 408 base pairs shorter, and Cq numbers were 1.9-2.4 higher. Using the FFPE extraction kit rescued yield and purity, but RIN further declined by 1.1 units. Differences between NBF+ve and NBF-ve in respect of DNA, histomorphology, and immunohistochemistry were either non-existent or small in magnitude. Formalin contamination of a tissue processor and its reagents therefore critically reduce RNA yield and integrity. We discuss the available options users can adopt to ameliorate this problem.
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Affiliation(s)
| | | | - Changyoung Yoo
- The Catholic University of Korea, St. Vincent's Hospital, Seoul, Korea
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5
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Nicoletti A, Pregel P, Starvaggi Cucuzza L, Cannizzo FT, Sereno A, Scaglione FE. Coping with Tissue Sampling in Suboptimal Conditions: Comparison of Different Tissue Preservation Methods for Histological and Molecular Analysis. Animals (Basel) 2021; 11:649. [PMID: 33804460 PMCID: PMC8001879 DOI: 10.3390/ani11030649] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 02/24/2021] [Accepted: 02/24/2021] [Indexed: 01/30/2023] Open
Abstract
A high quality of samples is crucial for the success of the analysis and diagnostic purposes, and therefore the right method of conservation is vitally important for an optimal preservation of tissues. Indeed, the time to deliver the sample to the laboratory could be remarkably long, especially under suboptimal conditions, and the use of specific fixatives or cold storage may not be possible. Moreover, the portability and cost of storage equipment, their toxicity, and their ease of use play a central role when choosing the correct preservation method. The aim of this study was the identification of a reliable and economic method for tissue preservation, to be used in "in-field" sampling, suitable for both histological and molecular analysis. Punch biopsies were collected from six cattle livers. Comparisons among methods of preservation using RNAlater, silica beads, and under-vacuum was carried out. These methods were tested through considering different times and temperatures, assuming three days as a maximum time interval from sampling to laboratory and choosing 4 °C and 24 °C as references for refrigeration temperature and room temperature, respectively. Histologically, the integrity of nucleus, cytoplasm, preservation of liver structure, and easiness of recognition of inflammatory infiltrate were evaluated. The integrity of the extracted DNA and RNA was evaluated through PCR and by means of an automated electrophoresis station, respectively. RNAlater and silica beads poorly preserved the histological parameters evaluated, independently from the temperature. Conversely, the vacuum-sealed samples showed a good grade of preservation until 48 h. DNA quality was acceptable for each sample. RNA integrity showed promising results only for samples preserved with silica beads.
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Affiliation(s)
- Arturo Nicoletti
- Department of Veterinary Sciences, University of Turin, Largo P. Braccini 2, 10095 Grugliasco, Italy; (P.P.); (L.S.C.); (F.T.C.); (A.S.); (F.E.S.)
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6
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Jensen PSH, Johansen M, Bak LK, Jensen LJ, Kjær C. Yield and Integrity of RNA from Brain Samples are Largely Unaffected by Pre-analytical Procedures. Neurochem Res 2020; 46:447-454. [PMID: 33249516 DOI: 10.1007/s11064-020-03183-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 11/13/2020] [Accepted: 11/17/2020] [Indexed: 11/28/2022]
Abstract
Gene expression studies are reported to be influenced by pre-analytical factors that can compromise RNA yield and integrity, which in turn may confound the experimental findings. Here we investigate the impact of four pre-analytical factors on brain-derived RNA: time-before-collection, tissue specimen size, tissue collection method, and RNA isolation method. We report no significant differences in RNA yield or integrity between 20 mg and 60 mg tissue samples collected in either liquid nitrogen or the RNAlater stabilizing solution. Isolation of RNA employing the TRIzol reagent resulted in a higher yield compared to isolation via the QIAcube kit while the latter resulted in RNA of slightly better integrity. Keeping brain tissue samples at room temperature for up to 160 min prior to collection and isolation of RNA resulted in no significant difference in yield or integrity. Our findings have significant practical and financial consequences for clinical genomic departments and other laboratory settings performing large-scale routine RNA expression analysis of brain samples.
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Affiliation(s)
- Pernille Søs Hovgaard Jensen
- Department of Technology, Faculty of Health and Technology, University College Copenhagen, 2200, Copenhagen, Denmark
| | - Maja Johansen
- Department of Technology, Faculty of Health and Technology, University College Copenhagen, 2200, Copenhagen, Denmark
| | - Lasse K Bak
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Lars Juhl Jensen
- Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Christina Kjær
- Department of Technology, Faculty of Health and Technology, University College Copenhagen, 2200, Copenhagen, Denmark. .,Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark.
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7
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Smith J, Faria CSAA, Qvist CC, Melchior LC, Lauridsen T. Prolonging fixation time of an alternative fixative to formalin for dermatological samples using standard laboratory protocols. J Clin Pathol 2020; 74:149-156. [PMID: 32669366 DOI: 10.1136/jclinpath-2020-206612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 05/15/2020] [Accepted: 05/28/2020] [Indexed: 11/03/2022]
Abstract
AIMS Though formalin remains to be the gold standard fixative in pathology departments, analytical challenges persist for nucleic acid evaluations. In our laboratory, formalin fixation of skin samples in particular impairs diagnostic accuracy and demands repetition of biopsies and analytical procedures. PAXgene Tissue Systems may be an alternative; however, according to manufacturer specifications it only allows fixation for 48 hours before having to add a stabiliser. This may be a challenge in laboratories, which are closed in weekends and bank holidays. Our aim was to validate this alternative fixative for dermatological samples with prolonged fixation times using standard laboratory protocols developed for formalin-fixed specimens. We compared the results with gold standard formalin fixation. METHODS Skin specimens were formalin or PAXgene fixed for either 2 hours, 24 hours, 3 days or 7 days, paraffin-embedded, analysed and scored by observers. RESULTS Generally, formalin outperformed PAXgene fixation in H&E stains and fluorescence in situ hybridisation (FISH), but both seem usable for diagnostics. Time of PAXgene fixation did not have an impact on alcian blue-Van Gieson (ABVG), H&E (p=0.48), nor immunohistochemistry (p=0.74). There was a tendency towards best PAXgene performance at 24 hours of fixation for FISH, and for DNA integrity analysis 24 hours or 3 days. CONCLUSIONS Prolonging PAXgene fixation time to 3 days before adding stabiliser does not seem to have major impact on performance of general diagnostic analysis, but our preliminary results show optimisation of internal protocols are needed. PAXgene is an expensive alternative and may be confined to some dermatological samples.
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Affiliation(s)
- Julie Smith
- Department of Technology, Faculty of Health and Technology, University College Copenhagen, Copenhagen, Denmark
| | | | - Camilla Christine Qvist
- Department of Pathology, Copenhagen University Hospital (Rigshospitalet), Copenhagen, Denmark
| | - Linea C Melchior
- Department of Pathology, Copenhagen University Hospital (Rigshospitalet), Copenhagen, Denmark
| | - Thomas Lauridsen
- Department of Pathology, Copenhagen University Hospital (Rigshospitalet), Copenhagen, Denmark.,Department of Pathology, Zealand University Hospital, Roskilde, Denmark
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8
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Taavela J, Viiri K, Popp A, Oittinen M, Dotsenko V, Peräaho M, Staff S, Sarin J, Leon F, Mäki M, Isola J. Histological, immunohistochemical and mRNA gene expression responses in coeliac disease patients challenged with gluten using PAXgene fixed paraffin-embedded duodenal biopsies. BMC Gastroenterol 2019; 19:189. [PMID: 31730447 PMCID: PMC6858741 DOI: 10.1186/s12876-019-1089-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 10/07/2019] [Indexed: 12/26/2022] Open
Abstract
Background There is an unmet need for novel treatments, such as drugs or vaccines, adjunctive to or replacing a burdensome life-long gluten-free diet for coeliac disease. The gold standard for successful treatment is a healed small intestinal mucosa, and therefore, the outcome measures in proof-of-concept studies should be based on evaluation of small intestine biopsies. We here evaluated morphometric, immunohistochemical and messenger RNA (mRNA) expression changes in coeliac disease patients challenged with gluten using PAXgene fixed paraffin-embedded biopsies. Methods Fifteen coeliac disease patients were challenged with 4 g of gluten per day for 10 weeks and 24 non-coeliac patients served as disease controls. A wide array of histological and immunohistochemical staining and mRNA-based gene expression tests (RT-qPCR and RNAseq) were carried out. Results Digital quantitative villous height: crypt depth ratio (VH: CrD) measurements revealed significant duodenal mucosal deterioration in all coeliac disease patients on gluten challenge. In contrast, the Marsh-Oberhuber class worsened in only 80% of coeliac patients. Measuring the intraepithelial CD3+ T-lymphocyte and lamina propria CD138+ plasma cell densities simultaneously proved to be a meaningful new measure of inflammation. Stainings for γδ T cells and IgA deposits, where previously frozen samples have been needed, were successful in PAXgene fixed paraffin-embedded samples. Messenger RNA extraction from the same paraffin-embedded biopsy block was successful and allowed large-scale qRT-PCR and RNAseq analyses for gene expression. Molecular morphometry, using the mRNA expression ratio of villous epithelium-specific gene APOA4 to crypt proliferation gene Ki67, showed a similar significant distinction between paired baseline and post-gluten challenge biopsies as quantitative histomorphometry. Conclusion Rigorous digitally measured histologic and molecular markers suitable for gluten challenge studies can be obtained from a single paraffin-embedded biopsy specimen. Molecular morphometry seems to be a promising new tool that can be used in situations where assessing duodenal mucosal health is of paramount importance. In addition, the diagnostically valuable IgA deposits were now stained in paraffin-embedded specimens making them more accessible in routine clinics.
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Affiliation(s)
- Juha Taavela
- Department of Paediatrics, Tampere Centre for Child Health Research, Faculty of Medicine and Health Technology, Tampere University, Tampere University Hospital, Tampere, Finland.,Department of Internal Medicine, Central Finland Central Hospital, Jyväskylä, Finland
| | - Keijo Viiri
- Department of Paediatrics, Tampere Centre for Child Health Research, Faculty of Medicine and Health Technology, Tampere University, Tampere University Hospital, Tampere, Finland
| | - Alina Popp
- Department of Paediatrics, Tampere Centre for Child Health Research, Faculty of Medicine and Health Technology, Tampere University, Tampere University Hospital, Tampere, Finland.,University of Medicine and Pharmacy "Carol Davila" and National Institute for Mother and Child Health "Alessandrescu-Rusescu", Bucharest, Romania
| | - Mikko Oittinen
- Department of Paediatrics, Tampere Centre for Child Health Research, Faculty of Medicine and Health Technology, Tampere University, Tampere University Hospital, Tampere, Finland
| | - Valeriia Dotsenko
- Department of Paediatrics, Tampere Centre for Child Health Research, Faculty of Medicine and Health Technology, Tampere University, Tampere University Hospital, Tampere, Finland
| | - Markku Peräaho
- Department of Internal Medicine, Central Finland Central Hospital, Jyväskylä, Finland
| | - Synnöve Staff
- Department of Gynaecology and Obstetrics, Tampere University Hospital, Tampere, Finland.,Laboratory of Cancer Biology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Jani Sarin
- Laboratory of Cancer Biology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,Jilab Inc., Tampere, Finland
| | | | - Markku Mäki
- Department of Paediatrics, Tampere Centre for Child Health Research, Faculty of Medicine and Health Technology, Tampere University, Tampere University Hospital, Tampere, Finland
| | - Jorma Isola
- Laboratory of Cancer Biology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland. .,Jilab Inc., Tampere, Finland.
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9
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Wang MM, Tan WJ, Lim TS, Chan ASY. PreservCyt Is an Optimal Fixative that Permits Cytologic and Molecular Analyses of Vitreoretinal Lymphoma Biopsies. Ocul Immunol Inflamm 2019; 29:430-439. [PMID: 31418635 DOI: 10.1080/09273948.2019.1636093] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Purpose: Vitreoretinal lymphoma (VRL) is a potentially fatal intraocular malignancy. Diagnosis is hampered by poor preservation of morphology and DNA/RNA integrity, which precludes adjunctive molecular analysis. We aimed to determine the optimum fixative protocol for VRL biopsies that permits cytology, IHC/flow cytometry and molecular analyses.Methods: Six fixatives were compared on cultured Pfeiffer cells used as a cellular model. Cells were fixed and evaluated on cellular morphology, antibody staining, DNA/RNA amount and integrity. VRL clinical cases were used as validation and proof-of-concept.Results: PreservCyt was the best fixative for preserving cellular morphology and high-quality RNA/DNA from vitreous fluid biopsies. Cells from clinical VRL cases fixed with PreservCyt showed adequate cellular morphology and IHC positivity. Sufficient DNA was obtained for IgH clonality and MYD88 mutation detection using remnant cytological fluid.Conclusions: PreservCyt maintains good morphology and RNA/DNA integrity suggesting that it is a suitable fixative for VRL diagnosis and molecular analysis.
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Affiliation(s)
- Mona Meng Wang
- Translational Ophthalmic Pathology Platform, Singapore Eye Research Institute, Singapore, Singapore
| | - Wei Jian Tan
- A. Menarini Biomarkers Singapore Pte Ltd, Singapore
| | | | - Anita Sook Yee Chan
- Translational Ophthalmic Pathology Platform, Singapore Eye Research Institute, Singapore, Singapore.,Ocular inflammation and Immunology Department, Singapore National Eye Centre, Singapore.,Ophthalmology & Visual Sciences Academic Clinical Program, Duke-NUS Medical School, Singapore
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10
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The impact of crosslinking and non-crosslinking fixatives on antigen retrieval and immunohistochemistry. N Biotechnol 2019; 52:69-83. [PMID: 31082574 DOI: 10.1016/j.nbt.2019.05.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 05/08/2019] [Accepted: 05/09/2019] [Indexed: 12/29/2022]
Abstract
Pre-analytical factors can greatly influence the outcome of molecular analyses in medical diagnostics and research. This also applies to in situ staining techniques such as immunohistochemistry (IHC), where different types of tissue fixation methods lead to different modifications of proteins and thus can affect differently the detection by antibodies. For formalin-fixed paraffin-embedded (FFPE) tissue, antigen retrieval is applied in order to reverse the negative effects of formalin and re-establish immunoreactivity. Most antibodies and protocols used in IHC are optimized for FFPE tissue, but not for paraffin-embedded tissue treated with other fixatives such as non-crosslinking fixatives. We report results from systematic studies on distinct pre-analytical conditions in IHC, immunofluorescence and electron microscopy. Parameters investigated are the impact of crosslinking and non-crosslinking fixatives (comparing formalin and PAXgene Tissue fixation) on whole tissue, subcellular structures and organelles, as well as on ultrastructure. The results generated show that minor changes in antigen retrieval conditions may have a major impact on IHC results and that protocols optimized for crosslinking fixatives may not be used for other fixatives without re-validation. Key antigen retrieval parameters such as buffers with different pH and duration of microwave treatment must be tested systematically for each antibody and fixation protocol.
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11
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Wang M, Ji X, Wang B, Li Q, Zhou J. Simultaneous Evaluation of the Preservative Effect of RNAlater on Different Tissues by Biomolecular and Histological Analysis. Biopreserv Biobank 2018; 16:426-433. [PMID: 30484701 DOI: 10.1089/bio.2018.0055] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
A major concern in biomedical research is the quality of biological samples. RNAlater is a stabilizer, which was originally developed for RNA preservation in fresh tissues and is important for collection and transportation. However, this reagent lacks a comprehensive and systematic evaluation of its preservative effect on different mammalian tissues under consistent experimental conditions. In this study, we collected liver, kidney, testis, brain, and colon tissues from mice and divided the samples into the following respective groups: fresh, RNAlater preserved, and liquid nitrogen snap frozen. Biomolecules (RNA, DNA, and protein) were extracted from each tissue in each group, and samples were formalin fixed and paraffin embedded for quality assessment. Our results revealed that high-quality (yield, purity, and integrity) nucleic acids could be extracted from all samples. Gene expression determined by quantitative real-time polymerase chain reaction exhibited no major difference among the three groups. Notably, we observed significant protein degradation in brain tissue preserved by RNAlater compared with fresh and snap-frozen tissue. Protein expression of the other four tissues was similar among the three groups. Hematoxylin and eosin staining of all tissue types indicated no apparent difference among the three groups. We concluded that high-quality nucleic acids can be obtained and tissue morphology conserved when tissues are preserved with RNAlater. However, there are tissue-specific differences in protein preservation when using RNAlater, which should be evaluated before extensive storage.
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Affiliation(s)
- Min Wang
- Department of Central Laboratory, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoli Ji
- Department of Central Laboratory, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Bingjie Wang
- Department of Central Laboratory, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Qian Li
- Department of Central Laboratory, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Junmei Zhou
- Department of Central Laboratory, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
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12
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Hutson HN, Kujawa C, Eliceiri K, Campagnola P, Masters KS. Impact of tissue preservation on collagen fiber architecture. Biotech Histochem 2018; 94:134-144. [PMID: 30354688 DOI: 10.1080/10520295.2018.1530373] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
Microarchitectural features of collagen-rich extracellular matrices provide the mechanical foundation for tissue function and exhibit topographical cues that influence cellular behavior including proliferation, migration and protein expression. Preservation of tissue microarchitecture is required for accurate evaluation of tissue characteristics and pathology. It is unclear whether common tissue preservation methods possess equal ability to preserve microarchitecture. We investigated collagen microarchitecture in samples that had been flash frozen, fixed in formalin or preserved in RNAlater®, and which contained both collagen-rich and collagen-sparse regions. Fibrillar collagen organization was characterized using picrosirius red staining and second harmonic generation (SHG) microscopy. Maintenance of collagen fiber characteristics compared to the gold standard of flash freezing depended on both the method of preservation and the local collagen content of the tissue. Both formalin fixation and RNAlater® preserved collagen fiber characteristics similar to flash freezing in collagen-rich areas of the tissue, but not in collagen-sparse regions. Analysis using picrosirius red staining indicated preservation-dependent changes in overall tissue architecture and suprafibrillar organization. Together with considerations of cost, ease of use, storage conditions and ability to use the preserved tissue for RNA or protein analysis, our quantitative characterization of the effects of preservation method on collagen microarchitecture may help investigators select the most appropriate preservation approach for their needs.
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Affiliation(s)
- H N Hutson
- a Department of Biomedical Engineering , University of Wisconsin-Madison , Madison , WI , USA
| | - C Kujawa
- a Department of Biomedical Engineering , University of Wisconsin-Madison , Madison , WI , USA
| | - K Eliceiri
- a Department of Biomedical Engineering , University of Wisconsin-Madison , Madison , WI , USA.,b Laboratory for Optical and Computational Instrumentation, Laboratory of Cell and Molecular Biology , University of Wisconsin-Madison , Madison , WI , USA
| | - P Campagnola
- a Department of Biomedical Engineering , University of Wisconsin-Madison , Madison , WI , USA
| | - K S Masters
- a Department of Biomedical Engineering , University of Wisconsin-Madison , Madison , WI , USA
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13
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Impact of storage conditions on the quality of nucleic acids in paraffin embedded tissues. PLoS One 2018; 13:e0203608. [PMID: 30192857 PMCID: PMC6128582 DOI: 10.1371/journal.pone.0203608] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 08/23/2018] [Indexed: 01/02/2023] Open
Abstract
RNA and DNA analyses from paraffin-embedded tissues (PET) are an important diagnostic tool for characterization of a disease, exploring biomarkers and treatment options. Since nucleic acids from formalin-fixed and paraffin-embedded (FFPE) tissue are of limited use for molecular analyses due to chemical modifications of biomolecules alternate, formalin-free fixation reagents such as the PAXgene Tissue system are of evolving interest. Furthermore, biomedical research and biomarker development critically relies on using long-term stored PET from medical archives or biobanks to correlate molecular features with long-term disease outcomes. We therefore performed a comparative study to evaluate the effect of long term storage of FFPE and PAXgene Tissue-fixed and paraffin-embedded (PFPE) tissue at different temperatures on nucleic acid stability and usability in PCR. Matched FFPE and PFPE human tissues from routine clinical setting or rat tissues from a highly controlled animal model were stored at room temperature and 4°C, as well as in case of animal tissues frozen at -20°C and -80°C. RNA and DNA were extracted in intervals for up to nine years, and examined for integrity, and usability in quantitative RT-PCR (RT-qPCR) or PCR (qPCR) assays. PET storage at room temperature led to a degradation of nucleic acids which was slowed down by storage at 4°C and prevented by storage at -20°C or -80°C. Degradation was associated with an amplicon length depending decrease of RT-qPCR and qPCR efficiency. Storage at 4°C improved amplifiability in RT-qPCR and qPCR profoundly. Chemically unmodified nucleic acids from PFPE tissue performed superior compared to FFPE tissue, regardless of storage time and temperature in both human and rat tissues. In conclusion molecular analyses from PET can be greatly improved by using a non-crosslinking fixative and storage at lower temperatures such as 4°C, which should be considered in prospective clinical studies.
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14
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Yamazaki M, Yabuki N, Suzuki Y, Ito M, Ikeda A, Natori O, Suzuki M, Kato A. PAXgene-fixed paraffin-embedded sample is applicable to laser capture microdissection with well-balanced RNA quality and tissue morphology. J Toxicol Pathol 2018; 31:213-220. [PMID: 30093792 PMCID: PMC6077159 DOI: 10.1293/tox.2017-0049] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 03/13/2018] [Indexed: 12/21/2022] Open
Abstract
Assessing how gene expression analysis by RNA sequencing (RNA-Seq) correlates to a unique morphology is increasingly necessary, and laser capture microdissection (LCM) is a critical research tool for discovering the genes responsible in a region of interest (ROI). Because RNA-Seq requires high-quality RNA, a sample preparation procedure that can preserve morphology and give the required quality of RNA is essential. A PAXgene®-fixed paraffin-embedded (XFPE) block can satisfy the need for high-quality RNA, but there are few reports on adapting the method for LCM, such as how small an ROI is analyzable by RNA-Seq. In this study, we confirmed the morphology and preservation of RNA in XFPE and then assessed the relationship between the size of pieces cut by LCM and their RNA quality. In XFPE, the morphology was similar to that in alcohol-based fixed samples, the quality of the RNA extracted from a whole sample was excellent, that is equivalent to that of a fresh frozen sample, and the quality was maintained over one year later. Three sizes of pieces—large (25,000 µm2), medium (5,000 µm2), and small (1,000 µm2)—were cut by LCM so that the total areas of the sections cut per size were the same. RNA quality was found to be best preserved when tissue was cut into pieces of over 5,000 µm2. In summary, XFPE exhibits good morphology and excellent preservation of RNA quality. Furthermore, it can be a good tool when used with LCM and RNA-Seq, giving well-balanced RNA quality and tissue morphology in the ROI.
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Affiliation(s)
- Masaki Yamazaki
- Research Division, Chugai Pharmaceutical Co., Ltd., 1-135 Komakado, Gotemba-shi, Shizuoka 412-8513, Japan
| | - Nami Yabuki
- Research Division, Chugai Pharmaceutical Co., Ltd., 1-135 Komakado, Gotemba-shi, Shizuoka 412-8513, Japan.,Forerunner Pharma Research Co., Ltd., Yokohama Bio Industry Center, 1-6 Suehiro-cho, Tsurumi-ku, Yokohama-shi, Kanagawa 230-0045, Japan
| | - Yasunori Suzuki
- Forerunner Pharma Research Co., Ltd., Yokohama Bio Industry Center, 1-6 Suehiro-cho, Tsurumi-ku, Yokohama-shi, Kanagawa 230-0045, Japan
| | - Mayumi Ito
- Forerunner Pharma Research Co., Ltd., Yokohama Bio Industry Center, 1-6 Suehiro-cho, Tsurumi-ku, Yokohama-shi, Kanagawa 230-0045, Japan
| | - Asuka Ikeda
- Chugai Research Institute for Medical Science, Inc., 1-135, Komakado, Gotemba-shi, Shizuoka 412-8513, Japan
| | - Osamu Natori
- Forerunner Pharma Research Co., Ltd., Yokohama Bio Industry Center, 1-6 Suehiro-cho, Tsurumi-ku, Yokohama-shi, Kanagawa 230-0045, Japan
| | - Masami Suzuki
- Research Division, Chugai Pharmaceutical Co., Ltd., 1-135 Komakado, Gotemba-shi, Shizuoka 412-8513, Japan.,Forerunner Pharma Research Co., Ltd., Yokohama Bio Industry Center, 1-6 Suehiro-cho, Tsurumi-ku, Yokohama-shi, Kanagawa 230-0045, Japan
| | - Atsuhiko Kato
- Research Division, Chugai Pharmaceutical Co., Ltd., 1-135 Komakado, Gotemba-shi, Shizuoka 412-8513, Japan
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15
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Kurnit KC, Dumbrava EEI, Litzenburger B, Khotskaya YB, Johnson AM, Yap TA, Rodon J, Zeng J, Shufean MA, Bailey AM, Sánchez NS, Holla V, Mendelsohn J, Shaw KM, Bernstam EV, Mills GB, Meric-Bernstam F. Precision Oncology Decision Support: Current Approaches and Strategies for the Future. Clin Cancer Res 2018; 24:2719-2731. [PMID: 29420224 PMCID: PMC6004235 DOI: 10.1158/1078-0432.ccr-17-2494] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 11/02/2017] [Accepted: 01/30/2018] [Indexed: 12/11/2022]
Abstract
With the increasing availability of genomics, routine analysis of advanced cancers is now feasible. Treatment selection is frequently guided by the molecular characteristics of a patient's tumor, and an increasing number of trials are genomically selected. Furthermore, multiple studies have demonstrated the benefit of therapies that are chosen based upon the molecular profile of a tumor. However, the rapid evolution of genomic testing platforms and emergence of new technologies make interpreting molecular testing reports more challenging. More sophisticated precision oncology decision support services are essential. This review outlines existing tools available for health care providers and precision oncology teams and highlights strategies for optimizing decision support. Specific attention is given to the assays currently available for molecular testing, as well as considerations for interpreting alteration information. This article also discusses strategies for identifying and matching patients to clinical trials, current challenges, and proposals for future development of precision oncology decision support. Clin Cancer Res; 24(12); 2719-31. ©2018 AACR.
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Affiliation(s)
- Katherine C Kurnit
- Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Beate Litzenburger
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Bioinformatics, Qiagen Inc., Redwood City, California
| | - Yekaterina B Khotskaya
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Amber M Johnson
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Timothy A Yap
- Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jordi Rodon
- Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jia Zeng
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Md Abu Shufean
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ann M Bailey
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Nora S Sánchez
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Vijaykumar Holla
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - John Mendelsohn
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Kenna Mills Shaw
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Elmer V Bernstam
- School of Biomedical Informatics and Medical School, The University of Texas Health Science Center at Houston, Houston, Texas
| | - Gordon B Mills
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Funda Meric-Bernstam
- Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas.
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Breast Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
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16
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Molecular Pathology and Pre-Analytic Variables: Impact on Clinical Practice From a Breast Pathology Perspective. CURRENT PATHOBIOLOGY REPORTS 2018. [DOI: 10.1007/s40139-018-0169-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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17
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Sanchez I, Betsou F, Culot B, Frasquilho S, McKay SC, Pericleous S, Smith C, Thomas G, Mathieson W. RNA and microRNA Stability in PAXgene-Fixed Paraffin-Embedded Tissue Blocks After Seven Years' Storage. Am J Clin Pathol 2018; 149:536-547. [PMID: 29659661 DOI: 10.1093/ajcp/aqy026] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES To evaluate the stability of RNA and microRNA (miRNA) in PAXgene-fixed paraffin-embedded tissue blocks after 7 years' storage. METHODS RNA and miRNA were extracted from PAXgene-fixed paraffin-embedded (PFPE) blocks in 2009 then stored at -80°C. Seven years later, RNA and miRNA were again extracted from the same blocks. RNA and miRNA integrity in the 2009 and 2016 extractions were compared using RNA integrity number (RIN), paraffin-embedded RNA metric (PERM), reverse transcription polymerase chain reaction (RT-PCR) for different amplicon lengths, and quantitative RT-PCR (qRT-PCR) for three mRNA and three miRNA targets. RESULTS In PFPE blocks, mRNA was poorer in 2016 extractions compared to the 2009 extractions in all blocks and all assays applied, with transcripts degrading at different rates in the same blocks. For miRNA, qRT-PCR showed no statistically significant differences between 2009 and 2016 extractions. CONCLUSIONS mRNA in PFPE tissue blocks degrades at room temperature storage over 7 years.
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Affiliation(s)
| | - Fay Betsou
- Integrated Biobank of Luxembourg, Dudelange, Luxembourg
| | | | | | - Siobhan C McKay
- Department of Surgery and Cancer, Imperial College London, London, UK
| | | | | | - Gerry Thomas
- Department of Surgery and Cancer, Imperial College London, London, UK
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18
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Ongay S, Langelaar-Makkinje M, Stoop MP, Liu N, Overkleeft H, Luider TM, Groothuis GMM, Bischoff R. Cleavable Crosslinkers as Tissue Fixation Reagents for Proteomic Analysis. Chembiochem 2018; 19:736-743. [PMID: 29356267 DOI: 10.1002/cbic.201700625] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Indexed: 12/17/2022]
Abstract
Formaldehyde fixation is widely used for long-term maintenance of tissue. However, due to formaldehyde-induced crosslinks, fixed tissue proteins are difficult to extract, which hampers mass spectrometry (MS) proteomic analyses. Recent years have seen the use of different combinations of high temperature and solubilizing agents (usually derived from antigen retrieval techniques) to unravel formaldehyde-fixed paraffin-embedded tissue proteomes. However, to achieve protein extraction yields similar to those of fresh-frozen tissue, high-temperature heating is necessary. Such harsh extraction conditions can affect sensitive amino acids and post-translational modifications, resulting in the loss of important information, while still not resulting in protein yields comparable to those of fresh-frozen tissue. Herein, the objective is to evaluate cleavable protein crosslinkers as fixatives that allow tissue preservation and efficient protein extraction from fixed tissue for MS proteomics under mild conditions. With this goal in mind, disuccinimidyl tartrate (DST) and dithiobis(succinimidylpropionate) (DSP) are investigated as cleavable fixating reagents. These compounds crosslink proteins by reacting with amino groups, leading to amide bond formation, and can be cleaved with sodium metaperiodate (cis-diols, DST) or reducing agents (disulfide bonds, DSP), respectively. Results show that cleavable protein crosslinking with DST and DSP allows tissue fixation with morphology preservation comparable to that of formaldehyde. In addition, cleavage of DSP improves protein recovery from fixed tissue by a factor of 18 and increases the number of identified proteins by approximately 20 % under mild extraction conditions compared with those of formaldehyde-fixed paraffin-embedded tissue. A major advantage of DSP is the introduction of well-defined protein modifications that can be taken into account during database searching. In contrast to DSP fixation, DST fixation followed by cleavage with sodium metaperiodate, although effective, results in side reactions that prevent effective protein extraction and interfere with protein identification. Protein crosslinkers that can be cleaved under mild conditions and result in defined modifications, such as DSP, are thus viable alternatives to formaldehyde as tissue fixatives to facilitate protein analysis from paraffin-embedded, fixed tissue.
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Affiliation(s)
- Sara Ongay
- Department of Analytical Biochemistry, University of Groningen, Antonius Deusinglaan 1, 9713, AV, Groningen, The Netherlands
| | - Miriam Langelaar-Makkinje
- Department Pharmacokinetics, Toxicology and Targeting, University of Groningen, Antonius Deusinglaan 1, 9713, AV, Groningen, The Netherlands
| | - Marcel P Stoop
- Department of Neurology, Erasmus University Medical Center, P. O. Box 1738, 3000 DR, Rotterdam, The Netherlands
| | - Nora Liu
- Department of Bio-Organic Synthesis, Leiden University, P. O. Box 9502, 2300 RA, Leiden, The Netherlands
| | - Hermen Overkleeft
- Department of Bio-Organic Synthesis, Leiden University, P. O. Box 9502, 2300 RA, Leiden, The Netherlands
| | - Theo M Luider
- Department of Neurology, Erasmus University Medical Center, P. O. Box 1738, 3000 DR, Rotterdam, The Netherlands
| | - Geny M M Groothuis
- Department Pharmacokinetics, Toxicology and Targeting, University of Groningen, Antonius Deusinglaan 1, 9713, AV, Groningen, The Netherlands
| | - Rainer Bischoff
- Department of Analytical Biochemistry, University of Groningen, Antonius Deusinglaan 1, 9713, AV, Groningen, The Netherlands
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19
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Steicke M, Yang G, Dinh TN, Dunster-Jones M, Sargisson O, Ahmady F, Golledge J, Wang Y. The penetration of methanol into bovine cardiac and hepatic tissues is faster than ethanol and formalin. Eur J Histochem 2018; 62:2880. [PMID: 29569879 PMCID: PMC5820526 DOI: 10.4081/ejh.2018.2880] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 02/01/2018] [Accepted: 02/01/2018] [Indexed: 11/23/2022] Open
Abstract
Methanol, ethanol and formalin are commonly used as fixatives to preserve biological tissues from decay in the preparation of histological sections. Fixation of the inner layers of the tissue depends on the ability of the fixative to diffuse into the tissue. It is unknown whether methanol penetrates tissues at similar rates to other fixatives. This study aimed to compare the penetration rates of methanol, ethanol and formalin into bovine heart and liver tissues. The penetration distance and tissue shrinkage or expansion were measured by analysing the digital images of tissue before and after immersion in different fixatives for 1, 2, 6 or 10 h. Data were analysed using two-way ANOVA, followed by Bonferroni's post-hoc test. The penetration distance of methanol was significantly greater in both heart and liver tissues compared with that of ethanol (N=4, P<0.001). Methanol or ethanol immersion led to similar shrinkage of both tissues (P>0.05). The penetration rate of formalin was similar to that of ethanol in both tissues however it was significantly slower than methanol (N=4, P<0.005 in the heart; P<0.001 in the liver). The mean penetration coefficients of methanol, formalin and ethanol in the heart tissue were 2.609, 1.994 and 1.801, respectively, and 3.012, 2.153 and 2.113, respectively, in the liver tissue. The penetration coefficient of methanol was significantly greater than that of ethanol or formalin in both tissues (P<0.001 for each comparison). In conclusion, methanol penetrates tissue significantly faster than ethanol and formalin.
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Affiliation(s)
- Michelle Steicke
- Federation University Australia, School of Applied and Biomedical Science.
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20
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Targeted Transcriptional Profiling of Kidney Transplant Biopsies. Kidney Int Rep 2018; 3:722-731. [PMID: 29854981 PMCID: PMC5976814 DOI: 10.1016/j.ekir.2018.01.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 01/30/2018] [Indexed: 02/06/2023] Open
Abstract
Introduction Studies are needed to assess the quality of transcriptome analysis in paired human tissue samples preserved by different methods and different gene amplification platforms to enable data comparisons across experimenters. Methods RNA was extracted from kidney biopsies, either submerged in RNA-stabilizing solution (RSS) or stored in formalin-fixed, paraffin-embedded (FFPE) blocks. RNA quality and integrity were compared. Gene expression of the common rejection module and other immune cell genes were quantified for both tissue preservation methods in the same sample using conventional quantitative polymerase chain reaction (QPCR) by 2 different commercial platforms, (fluidigm [FD]) or barcoded-oligos (nanostring [NS]). Results RNA quality was inferior in FFPE tissues. Despite this, gene expression for 19 measured genes on the same sample, stored in FFPE or RSS, were strongly correlated on the FD (r = 0.81) or NS platforms (r = 0.82). For the same samples, interplatform gene expression correlations were excellent (r = 0.80) for RSS and moderate (r = 0.66) for FFPE. Significant differences in gene expression were confirmed on both platforms (FD: P = 1.1E-03; NS: P = 2.5E-04) for biopsy-confirmed acute rejection. Conclusion Our study provided supportive evidence that despite a low RNA quality of archival FFPE kidney transplantation tissue, small quantities of this tissue can be obtained from existing paraffin blocks to provide a viable and rich biospecimen source for focused gene expression assays. In addition, reliable and reproducible gene expression evaluation can be performed on these FFPE tissues using either a QPCR-based or a barcoded-oligo approach, which provides opportunities for collaborative analytics.
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21
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Cummings M, Mappa G, Orsi NM. Laser Capture Microdissection and Isolation of High-Quality RNA from Frozen Endometrial Tissue. Methods Mol Biol 2018; 1723:155-166. [PMID: 29344859 DOI: 10.1007/978-1-4939-7558-7_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2023]
Abstract
Laser capture microdissection (LCM) allows expression profiling of specific cell populations within tissues. However, isolation of high-quality RNA from laser capture microdissected frozen tissue is beset by problems arising from intrinsic tissue RNase activity. Herein, we describe an optimized staining/LCM/RNA extraction protocol developed for the isolation of epithelial RNA from frozen tissue sections using human endometrial cancer as a model tissue. This method combines excellent, reproducible visualization of tissue morphology with the isolation of high-integrity RNA suitable for downstream applications such as expression microarray analysis. We present quantitative and qualitative RNA data obtained from >200 endometrial epithelial samples (normal, hyperplastic, and cancerous), where 92% of samples had RIN values of 7 and above and highlight common pitfalls faced by investigators. This method should also be broadly applicable to a range of other tissue types.
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Affiliation(s)
- Michele Cummings
- Leeds Institute of Cancer and Pathology, St. James's University Hospital, Leeds, UK
| | - Georgia Mappa
- Leeds Institute of Cancer and Pathology, St. James's University Hospital, Leeds, UK
| | - Nicolas M Orsi
- Leeds Institute of Cancer and Pathology, St. James's University Hospital, Leeds, UK.
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22
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Högnäs G, Kivinummi K, Kallio HML, Hieta R, Ruusuvuori P, Koskenalho A, Kesseli J, Tammela TLJ, Riikonen J, Ilvesaro J, Kares S, Hirvikoski PP, Laurila M, Mirtti T, Nykter M, Kujala PM, Visakorpi T, Tolonen T, Bova GS. Feasibility of Prostate PAXgene Fixation for Molecular Research and Diagnostic Surgical Pathology: Comparison of Matched Fresh Frozen, FFPE, and PFPE Tissues. Am J Surg Pathol 2017; 42:103-115. [PMID: 28984675 DOI: 10.1097/pas.0000000000000961] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Advances in prostate cancer biology and diagnostics are dependent upon high-fidelity integration of clinical, histomorphologic, and molecular phenotypic findings. In this study, we compared fresh frozen, formalin-fixed paraffin-embedded (FFPE), and PAXgene-fixed paraffin-embedded (PFPE) tissue preparation methods in radical prostatectomy prostate tissue from 36 patients and performed a preliminary test of feasibility of using PFPE tissue in routine prostate surgical pathology diagnostic assessment. In addition to comparing histology, immunohistochemistry, and general measures of DNA and RNA integrity in each fixation method, we performed functional tests of DNA and RNA quality, including targeted Miseq RNA and DNA sequencing, and implemented methods to relate DNA and RNA yield and quality to quantified DNA and RNA picogram nuclear content in each tissue volume studied. Our results suggest that it is feasible to use PFPE tissue for routine robot-assisted laparoscopic prostatectomy surgical pathology diagnostics and immunohistochemistry, with the benefit of significantly improvedDNA and RNA quality and RNA picogram yield per nucleus as compared with FFPE tissue. For fresh frozen, FFPE, and PFPE tissues, respectively, the average Genomic Quality Numbers were 7.9, 3.2, and 6.2, average RNA Quality Numbers were 8.7, 2.6, and 6.3, average DNA picogram yields per nucleus were 0.41, 0.69, and 0.78, and average RNA picogram yields per nucleus were 1.40, 0.94, and 2.24. These findings suggest that where DNA and/or RNA analysis of tissue is required, and when tissue size is small, PFPE may provide important advantages over FFPE. The results also suggest several interesting nuances including potential avenues to improve RNA quality in FFPE tissues and confirm recent suggestions that some DNA sequence artifacts associated with FFPE can be avoided.
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Affiliation(s)
- Gunilla Högnäs
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute
| | - Kati Kivinummi
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute
| | - Heini M L Kallio
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute
| | - Reija Hieta
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute
| | - Pekka Ruusuvuori
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute.,Signal Processing Laboratory, Tampere University of Technology, Pori
| | - Antti Koskenalho
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute
| | - Juha Kesseli
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute
| | - Teuvo L J Tammela
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute.,Department of Urology, University of Tampere
| | | | - Joanna Ilvesaro
- Fimlab Laboratories, Department of Pathology, Tampere University Hospital, Tampere
| | - Saara Kares
- Fimlab Laboratories, Department of Pathology, Tampere University Hospital, Tampere
| | | | - Marita Laurila
- Fimlab Laboratories, Department of Pathology, Tampere University Hospital, Tampere
| | - Tuomas Mirtti
- Institute for Molecular Medicine Finland, University of Helsinki.,Department of Pathology, HUSLAB, Helsinki University Hospital, Helsinki, Finland
| | - Matti Nykter
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute
| | - Paula M Kujala
- Fimlab Laboratories, Department of Pathology, Tampere University Hospital, Tampere
| | - Tapio Visakorpi
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute.,Fimlab Laboratories, Department of Pathology, Tampere University Hospital, Tampere
| | - Teemu Tolonen
- Fimlab Laboratories, Department of Pathology, Tampere University Hospital, Tampere
| | - G Steven Bova
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute
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23
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Reid KM, Maistry S, Ramesar R, Heathfield LJ. A review of the optimisation of the use of formalin fixed paraffin embedded tissue for molecular analysis in a forensic post-mortem setting. Forensic Sci Int 2017; 280:181-187. [PMID: 29078160 DOI: 10.1016/j.forsciint.2017.09.020] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 07/15/2017] [Accepted: 09/26/2017] [Indexed: 11/26/2022]
Abstract
Molecular analyses in a post-mortem setting are becoming increasingly common, particularly in cases of sudden unexplained death, with the aim of identifying genetic mutations which may be responsible for causing death. In retrospective investigations, the access to suitable autopsy biological samples may be limited, and often formalin fixed paraffin embedded (FFPE) tissue is the only sample available. The preservation of tissue in formalin is known to damage DNA through crosslinking activity. This results in the extraction of severely fragmented DNA of variable yields, which subsequently reduces the ability to perform downstream molecular analyses. Numerous studies have investigated possible improvements to various aspects of the DNA extraction and amplification procedures from FFPE tissue and this review aims to collate these optimization steps in a cohesive manner. A systematic review was performed of three major databases, which identified 111 articles meeting the inclusion criteria. Five main areas for optimization and improvements were identified in the workflow: (1) tissue type, (2) fixation process, (3) post-fixation, (4) DNA extraction procedure and (5) amplification. It was found that some factors identified, for example tissue type and fixation process, could not be controlled by the researcher when conducting retrospective analyses. For this reason, optimization should be performed in other areas, within the financial means of the laboratories, and in accordance with the purposes of the investigation. Implementation of one or more of the optimization measures described here is anticipated to assist in the extraction of higher quality DNA. Despite the challenges posed by FFPE tissue, it remains a valuable source of DNA in retrospective molecular forensic investigations.
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Affiliation(s)
- Kate Megan Reid
- Division of Forensic Medicine and Toxicology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory, 7925, South Africa; MRC/UCT Human Genetics Research Unit, Division of Human Genetics, Department of Pathology, Institute of Infectious Diseases and Molecular Medicine, Faculty of Health Science, University of Cape Town, Anzio Road, Observatory, Cape Town, South Africa
| | - Sairita Maistry
- Division of Forensic Medicine and Toxicology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory, 7925, South Africa
| | - Raj Ramesar
- MRC/UCT Human Genetics Research Unit, Division of Human Genetics, Department of Pathology, Institute of Infectious Diseases and Molecular Medicine, Faculty of Health Science, University of Cape Town, Anzio Road, Observatory, Cape Town, South Africa
| | - Laura Jane Heathfield
- Division of Forensic Medicine and Toxicology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory, 7925, South Africa; MRC/UCT Human Genetics Research Unit, Division of Human Genetics, Department of Pathology, Institute of Infectious Diseases and Molecular Medicine, Faculty of Health Science, University of Cape Town, Anzio Road, Observatory, Cape Town, South Africa.
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Stewart JP, Richman S, Maughan T, Lawler M, Dunne PD, Salto-Tellez M. Standardising RNA profiling based biomarker application in cancer-The need for robust control of technical variables. Biochim Biophys Acta Rev Cancer 2017; 1868:258-272. [PMID: 28549623 DOI: 10.1016/j.bbcan.2017.05.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 05/21/2017] [Accepted: 05/22/2017] [Indexed: 01/10/2023]
Abstract
Histopathology-based staging of colorectal cancer (CRC) has utility in assessing the prognosis of patient subtypes, but as yet cannot accurately predict individual patient's treatment response. Transcriptomics approaches, using array based or next generation sequencing (NGS) platforms, of formalin fixed paraffin embedded tissue can be harnessed to develop multi-gene biomarkers for predicting both prognosis and treatment response, leading to stratification of treatment. While transcriptomics can shape future biomarker development, currently <1% of published biomarkers become clinically validated tests, often due to poor study design or lack of independent validation. In this review of a large number of CRC transcriptional studies, we identify recurrent sources of technical variability that encompass collection, preservation and storage of malignant tissue, nucleic acid extraction, methods to quantitate RNA transcripts and data analysis pipelines. We propose a series of defined steps for removal of these confounding issues, to ultimately aid in the development of more robust clinical biomarkers.
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Affiliation(s)
- James P Stewart
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, UK; Northern Ireland Molecular Pathology Laboratory, Queen's University Belfast, UK
| | - Susan Richman
- Department of Pathology and Tumour Biology, St James University Hospital, Leeds, UK
| | - Tim Maughan
- CRUK/MRC Oxford Institute for Radiation Oncology, University of Oxford, UK
| | - Mark Lawler
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, UK
| | - Philip D Dunne
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, UK
| | - Manuel Salto-Tellez
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, UK; Northern Ireland Molecular Pathology Laboratory, Queen's University Belfast, UK.
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KINFix--A formalin-free non-commercial fixative optimized for histological, immunohistochemical and molecular analyses of neurosurgical tissue specimens. Clin Neuropathol 2016; 35:3-12. [PMID: 26521938 PMCID: PMC4766796 DOI: 10.5414/np300907] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/16/2015] [Indexed: 12/04/2022] Open
Abstract
An optimal fixative should ideally combine the advantages of formalin fixation and freezing, allowing for good preservation of histology and molecular components, easy handling and storage, lack of toxicity, and low costs. Most of these criteria are fulfilled by ethanol-based solutions, and due to our good experience with the commercial RCL2 fixative, reflected by our published single-center trial, we initiated a multicenter ring trial. However, during its course, RCL2 was discontinued on the market. Therefore, we created our own agent, KINFix, composed of the same main constituents as RCL2, and employed it in our laboratory with similar results. Here we present our evaluation of the three fixatives formalin, RCL2, and KINFix from the perspective of histopathology as well as nucleic acid and protein analyses in comparison to fresh frozen tissues together with the multicenter ring trial data for RCL2. We observe that RCL2 and KINFix offer comparable histomorphology and superior template for molecular analyses than formalin. Moreover, KINFix as freely available fixative might overcome some of the difficulties related to the commercial agents. Therefore, we conclude that KINFix might be an attractive complement to formalin in tissue processing and advocate its use in neuropathological practice.
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Bridge JA. Reverse transcription-polymerase chain reaction molecular testing of cytology specimens: Pre-analytic and analytic factors. Cancer Cytopathol 2016; 125:11-19. [DOI: 10.1002/cncy.21762] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 06/22/2016] [Accepted: 06/23/2016] [Indexed: 01/02/2023]
Affiliation(s)
- Julia A. Bridge
- Department of Pathology and Microbiology; University of Nebraska Medical Center; Omaha Nebraska
- Department of Pediatrics; University of Nebraska Medical Center; Omaha Nebraska
- Department of Orthopedic Surgery; University of Nebraska Medical Center; Omaha Nebraska
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Liu Y, Edward DP. Assessment of PAXgene Fixation on Preservation of Morphology and Nucleic Acids in Microdissected Retina Tissue. Curr Eye Res 2016; 42:104-110. [DOI: 10.3109/02713683.2016.1146777] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Mathieson W, Marcon N, Antunes L, Ashford DA, Betsou F, Frasquilho SG, Kofanova OA, McKay SC, Pericleous S, Smith C, Unger KM, Zeller C, Thomas GA. A Critical Evaluation of the PAXgene Tissue Fixation System: Morphology, Immunohistochemistry, Molecular Biology, and Proteomics. Am J Clin Pathol 2016; 146:25-40. [PMID: 27402607 DOI: 10.1093/ajcp/aqw023] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES To evaluate the PAXgene tissue fixation system. METHODS Clinical biospecimens (n = 46) were divided into PAXgene-fixed paraffin-embedded (PFPE), formalin-fixed paraffin-embedded (FFPE), and fresh-frozen (FF) blocks. PFPE and FFPE sections were compared for histology (H&E staining) and immunohistochemistry (14 antibodies) using tissue microarrays. PFPE, FFPE, and FF samples were compared in terms of RNA quality (RNA integrity number, polymerase chain reaction [PCR] amplicon length, and quantitative reverse transcription PCR), DNA quality (gel electrophoresis and methylation profiling) and protein quality (liquid chromatography-mass spectrometry [LC-MS/MS]). RESULTS PFPE protocol optimization was required in most cases and is described. RNA extracted from PFPE sections was considerably less degraded than that from FFPE sections but more degraded than that from FF blocks. Genomic-length DNA was extracted from PFPE and FF biospecimens, and methylation profiling showed PFPE and FF biospecimens to be almost indistinguishable. Only degraded DNA was extracted from FFPE biospecimens. PFPE sections yielded peptides that were slightly less amenable to LC-MS/MS analysis than FFPE sections, but FF gave slightly better results. CONCLUSIONS While it cannot be envisaged that PAXgene will replace formalin in a routine clinical setting, for specific projects or immunodiagnostics involving biospecimens destined for immunohistochemical or histologic staining and DNA or RNA analyses, PAXgene is a viable option.
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Affiliation(s)
- William Mathieson
- From the Integrated Biobank of Luxembourg, Luxembourg
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | | | | | - David A. Ashford
- Bioscience Technology Facility, Department of Biology, University of York, York, United Kingdom
| | - Fay Betsou
- From the Integrated Biobank of Luxembourg, Luxembourg
| | | | | | - Siobhan C. McKay
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Stephan Pericleous
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Colleen Smith
- Wales Cancer Bank, Singleton Hospital, Swansea, United Kingdom
| | - Kristian M. Unger
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Constanze Zeller
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Geraldine A. Thomas
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
- Wales Cancer Bank, Singleton Hospital, Swansea, United Kingdom
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Clinical impact of targeted amplicon sequencing for meningioma as a practical clinical-sequencing system. Mod Pathol 2016; 29:708-16. [PMID: 27102344 DOI: 10.1038/modpathol.2016.81] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 03/21/2016] [Accepted: 03/24/2016] [Indexed: 11/08/2022]
Abstract
Recent genetic analyses using next-generation sequencers have revealed numerous genetic alterations in various tumors including meningioma, which is the most common primary brain tumor. However, their use as routine laboratory examinations in clinical applications for tumor genotyping is not cost effective. To establish a clinical sequencing system for meningioma and investigate the clinical significance of genotype, we retrospectively performed targeted amplicon sequencing on 103 meningiomas and evaluated the association with clinicopathological features. We designed amplicon-sequencing panels targeting eight genes including NF2 (neurofibromin 2), TRAF7, KLF4, AKT1, and SMO. Libraries prepared with genomic DNA extracted from PAXgene-fixed paraffin-embedded tissues of 103 meningioma specimens were sequenced using the Illumina MiSeq. NF2 loss in some cases was also confirmed by interphase-fluorescent in situ hybridization. We identified NF2 loss and/or at least one mutation in NF2, TRAF7, KLF4, AKT1, and SMO in 81 out of 103 cases (79%) by targeted amplicon sequencing. On the basis of genetic status, we categorized meningiomas into three genotype groups: NF2 type, TRAKLS type harboring mutation in TRAF7, AKT1, KLF4, and/or SMO, and 'not otherwise classified' type. Genotype significantly correlated with tumor volume, tumor location, and magnetic resonance imaging findings such as adjacent bone change and heterogeneous gadolinium enhancement, as well as histopathological subtypes. In addition, multivariate analysis revealed that genotype was independently associated with risk of recurrence. In conclusion, we established a rapid clinical sequencing system that enables final confirmation of meningioma genotype within 7 days turnaround time. Our method will bring multiple benefits to neuropathologists and neurosurgeons for accurate diagnosis and appropriate postoperative management.
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Loibner M, Buzina W, Viertler C, Groelz D, Hausleitner A, Siaulyte G, Kufferath I, Kölli B, Zatloukal K. Pathogen Inactivating Properties and Increased Sensitivity in Molecular Diagnostics by PAXgene, a Novel Non-Crosslinking Tissue Fixative. PLoS One 2016; 11:e0151383. [PMID: 26974150 PMCID: PMC4790970 DOI: 10.1371/journal.pone.0151383] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 02/26/2016] [Indexed: 11/20/2022] Open
Abstract
Background Requirements on tissue fixatives are getting more demanding as molecular analysis becomes increasingly relevant for routine diagnostics. Buffered formaldehyde in pathology laboratories for tissue fixation is known to cause chemical modifications of biomolecules which affect molecular testing. A novel non-crosslinking tissue preservation technology, PAXgene Tissue (PAXgene), was developed to preserve the integrity of nucleic acids in a comparable way to cryopreservation and also to preserve morphological features comparable to those of formalin fixed samples. Methods Because of the excellent preservation of biomolecules by PAXgene we investigated its pathogen inactivation ability and biosafety in comparison to formalin by in-vitro testing of bacteria, human relevant fungi and human cytomegalovirus (CMV). Guidelines for testing disinfectants served as reference for inactivation assays. Furthermore, we tested the properties of PAXgene for detection of pathogens by PCR based assays. Results All microorganisms tested were similarly inactivated by PAXgene and formalin except Clostridium sporogenes, which remained viable in seven out of ten assays after PAXgene treatment and in three out of ten assays after formalin fixation. The findings suggest that similar biosafety measures can be applied for PAXgene and formalin fixed samples. Detection of pathogens in PCR-based diagnostics using two CMV assays resulted in a reduction of four to ten quantification cycles of PAXgene treated samples which is a remarkable increase of sensitivity. Conclusion PAXgene fixation might be superior to formalin fixation when molecular diagnostics and highly sensitive detection of pathogens is required in parallel to morphology assessment.
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Affiliation(s)
- Martina Loibner
- Christian Doppler Laboratory for Biospecimen Research and Biobanking Technologies, Institute of Pathology, Medical University Graz, Graz, Austria
- Medical University Graz, Institute of Pathology, Graz, Austria
| | - Walter Buzina
- Medical University Graz, Institute of Hygiene, Microbiology and Environmental Medicine, Graz, Austria
| | | | - Daniel Groelz
- Qiagen GmbH, Research and Development, Hilden, Germany
| | - Anja Hausleitner
- Christian Doppler Laboratory for Biospecimen Research and Biobanking Technologies, Institute of Pathology, Medical University Graz, Graz, Austria
- LKH Hospital Weiz, Laboratory of Medical Department, Weiz, Austria
| | - Gintare Siaulyte
- Christian Doppler Laboratory for Biospecimen Research and Biobanking Technologies, Institute of Pathology, Medical University Graz, Graz, Austria
- Medical University Graz, Institute of Pathology, Graz, Austria
| | - Iris Kufferath
- Christian Doppler Laboratory for Biospecimen Research and Biobanking Technologies, Institute of Pathology, Medical University Graz, Graz, Austria
- Medical University Graz, Institute of Pathology, Graz, Austria
| | - Bettina Kölli
- Medical University Graz, Institute of Hygiene, Microbiology and Environmental Medicine, Graz, Austria
| | - Kurt Zatloukal
- Christian Doppler Laboratory for Biospecimen Research and Biobanking Technologies, Institute of Pathology, Medical University Graz, Graz, Austria
- Medical University Graz, Institute of Pathology, Graz, Austria
- * E-mail:
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Lung J, Lin YC, Hung MS, Jiang YY, Lee KD, Lin PY, Tsai YH. A sensitive and high throughput TaqMan-based reverse transcription quantitative polymerase chain reaction assay efficiently discriminates ALK rearrangement from overexpression for lung cancer FFPE specimens. Lung Cancer 2016; 94:114-20. [PMID: 26973216 DOI: 10.1016/j.lungcan.2016.02.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 02/03/2016] [Accepted: 02/06/2016] [Indexed: 12/18/2022]
Abstract
OBJECTIVES ALK fusion gene is an oncogenic driver in lung cancer with low prevalence, which can be ameliorated by crizotinib. Currently, ALK fusion gene can be diagnosed by fluorescence in situ hybridization (FISH) and immunohistochemistry (IHC), but inconstistnt results between the two methods are encountered regularly. To make the ALK fusion gene screening more efficient and to provide a simple solution to clarify the discrepancy between FISH and IHC results, a sensitive TaqMan-based reverse transcription quantitative polymerase chain reaction (RT-qPCR) assay was established. MATERIALS AND METHODS The 3-plex TaqMan-based RT-qPCR assay was established and performed on 102 archived formalin-fixed, paraffin-embedded (FFPE) NSCLC samples to detect ALK rearrangement and overexpression. Break-apart FISH and automatic immunohistochemistry based ALK assays were performed side by side using tissue microarray. RESULTS The RT-qPCR was performed successfully for 80 samples and 10 of them showed positive signals. Three out of the 10 qPCR positive cases were further confirmed by FISH and IHC test. Two others were IHC positive and FISH negative, and expressed full-length ALK transcript. The rest were neither FISH nor IHC positive and their ALK expression level was significantly lower than those FISH or IHC positive cases. CONCLUSION Our RT-qPCR assay demonstrates that the capability and reliability of ALK detection is comparable to FISH and IHC, but it is more effective at discriminating ALK rearrangement from overexpression. The RT-qPCR assay easily clarifies the discrepancy between FISH and IHC, and can be incorporated into routine ALK screening for lung cancer.
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Affiliation(s)
- Jrhau Lung
- Department of Medical Research and Development, Chang Gung Memorial Hospital, Chiayi branch, Taiwan
| | - Yu-Ching Lin
- Division of Thoracic Oncology, Department of Pulmonary and Critical Care Medicine, Chang Gung Memorial Hospital, Chiayi branch, Taiwan; Department of Medicine, College of Medicine, Chang Gung University, Taoyuan, Taiwan; Department of Respiratory Care, Chang Gung University of Science and Technology, Chiayi Campus, Chiayi, Taiwan
| | - Ming-Szu Hung
- Division of Thoracic Oncology, Department of Pulmonary and Critical Care Medicine, Chang Gung Memorial Hospital, Chiayi branch, Taiwan; Department of Medicine, College of Medicine, Chang Gung University, Taoyuan, Taiwan; Department of Respiratory Care, Chang Gung University of Science and Technology, Chiayi Campus, Chiayi, Taiwan
| | - Yuan Yuan Jiang
- Division of Thoracic Oncology, Department of Pulmonary and Critical Care Medicine, Chang Gung Memorial Hospital, Chiayi branch, Taiwan
| | - Kuan-Der Lee
- Department of Medicine, College of Medicine, Chang Gung University, Taoyuan, Taiwan; Hematology and Oncology, Chang Gung Memorial Hospital, Chiayi branch, Taiwan
| | - Paul Yann Lin
- Department of Pathology, Chang Gung Memorial Hospital, Chiayi branch, Taiwan
| | - Ying Huang Tsai
- Division of Thoracic Oncology, Department of Pulmonary and Critical Care Medicine, Chang Gung Memorial Hospital, Chiayi branch, Taiwan; Department of Respiratory Care, College of Medicine, Chang Gung University, Taoyuan, Taiwan.
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Noehammer C, Pulverer W, Hassler MR, Hofner M, Wielscher M, Vierlinger K, Liloglou T, McCarthy D, Jensen TJ, Nygren A, Gohlke H, Trooskens G, Braspenning M, Van Criekinge W, Egger G, Weinhaeusel A. Strategies for validation and testing of DNA methylation biomarkers. Epigenomics 2015; 6:603-22. [PMID: 25531255 DOI: 10.2217/epi.14.43] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
DNA methylation is a stable covalent epigenetic modification of primarily CpG dinucleotides that has recently gained considerable attention for its use as a biomarker in different clinical settings, including disease diagnosis, prognosis and therapeutic response prediction. Although the advent of genome-wide DNA methylation profiling in primary disease tissue has provided a manifold resource for biomarker development, only a tiny fraction of DNA methylation-based assays have reached clinical testing. Here, we provide a critical overview of different analytical methods that are suitable for biomarker validation, including general study design considerations, which might help to streamline epigenetic marker development. Furthermore, we highlight some of the recent marker validation studies and established markers that are currently commercially available for assisting in clinical management of different cancers.
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Affiliation(s)
- Christa Noehammer
- Health & Environment Department, Molecular Diagnostics, AIT Austrian Institute of Technology, Vienna, Austria
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Väänänen RM, Ochoa NT, Boström PJ, Taimen P, Pettersson K. Altered PCA3 and TMPRSS2-ERG expression in histologically benign regions of cancerous prostates: a systematic, quantitative mRNA analysis in five prostates. BMC Urol 2015; 15:88. [PMID: 26294063 PMCID: PMC4546243 DOI: 10.1186/s12894-015-0077-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 07/31/2015] [Indexed: 11/10/2022] Open
Abstract
Background PCA3 and TMPRSS2-ERG are commonly overexpressed biomarkers in prostate cancer, but reports have emerged demonstrating altered expression also in areas outside the tumour foci in cancerous prostates. Our aim was to measure PCA3 and TMPRSS2-ERG expression systematically in all regions of prostate cross-sections, matching the data to corresponding tissue morphology. Methods TMPRSS2-ERG and PCA3 mRNA levels were measured with quantitative reverse-transcription PCR assays in 270 samples from cross-sections of five radical prostatectomy specimens. ERG expression was examined by immunohistochemistry. Results TMPRSS2-ERG mRNAs were detected in three patients and in 15 tissue samples in total. These included two carcinoma samples and 13 histologically benign samples, eight of which were located next to malignant tumours or PIN (prostatic intraepithelial neoplasia) lesions and five of which did not reside in the vicinity of any evident carcinoma foci. ERG protein expression was limited to areas of TMPRSS2-ERG mRNA expression, but did not identify all of them. PCA3 expression was detected in all five cross-sections, with statistically significant, three-fold higher expression in carcinoma regions. Conclusions TMPRSS2-ERG expression was detected in carcinoma foci, regions next to them, and in samples not adjacent to carcinoma foci. Claimed as a cancer-associated phenomenon, this fusion gene measurement could, if validated with a larger cohort, be utilized as an addition to histological analysis to predict current or future cancer risk in men with negative biopsies. Molecular changes outside the carcinoma foci are also indicated for PCA3, as its expression was only moderately increased in the carcinoma regions.
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Affiliation(s)
| | | | - Peter J Boström
- Department of Urology, Turku University Hospital, Turku, Finland.
| | - Pekka Taimen
- Department of Pathology, University of Turku and Turku University Hospital, Turku, Finland.
| | - Kim Pettersson
- Department of Biotechnology, University of Turku, Turku, Finland.
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Greytak SR, Engel KB, Bass BP, Moore HM. Accuracy of Molecular Data Generated with FFPE Biospecimens: Lessons from the Literature. Cancer Res 2015; 75:1541-7. [PMID: 25836717 DOI: 10.1158/0008-5472.can-14-2378] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 12/22/2014] [Indexed: 12/15/2022]
Abstract
Formalin-fixed and paraffin-embedded (FFPE) tissue biospecimens are a valuable resource for molecular cancer research. Although much can be gained from their use, it remains unclear whether the genomic and expression profiles obtained from FFPE biospecimens accurately reflect the physiologic condition of the patient from which they were procured, or if such profiles are confounded by biologic effects from formalin fixation and processing. To assess the physiologic accuracy of genomic and expression data generated with FFPE specimens, we surveyed the literature for articles investigating genomic and expression endpoints in case-matched FFPE and fresh or frozen human biospecimens using the National Cancer Institute's Biospecimen Research Database (http://biospecimens.cancer.gov/brd). Results of the survey revealed that the level of concordance between differentially preserved biospecimens varied among analytical parameters and platforms but also among reports, genes/transcripts of interest, and tumor status. The identified analytical techniques and parameters that resulted in strong correlations between FFPE and frozen biospecimens may provide guidance when optimizing molecular protocols for FFPE use; however, discrepancies reported for similar assays also illustrate the importance of validating protocols optimized for use with FFPE specimens with a case-matched fresh or frozen cohort for each platform, gene or transcript, and FFPE processing regime. On the basis of evidence published to date, validation of analytical parameters with a properly handled frozen cohort is necessary to ensure a high degree of concordance and confidence in the results obtained with FFPE biospecimens.
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Affiliation(s)
| | | | | | - Helen M Moore
- Biorepositories and Biospecimen Research Branch, Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland.
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Clinical characteristics of women diagnosed with carcinoma who tested positive for cervical and anal high-risk human papillomavirus DNA and E6 RNA. Tumour Biol 2015; 36:5399-405. [PMID: 25677903 DOI: 10.1007/s13277-015-3205-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Accepted: 02/03/2015] [Indexed: 12/18/2022] Open
Abstract
High-risk human papillomavirus (hrHPV) is an essential cause of cervical carcinoma and is also strongly related to anal cancer development. The hrHPV E6 oncoprotein plays a major role in carcinogenesis. We aimed to evaluate the frequency of hrHPV DNA and E6 oncoprotein in the anuses of women with cervical carcinoma. We analyzed 117 women with cervical cancer and 103 controls for hrHPV and the E6 oncogene. Positive test results for a cervical carcinoma included 66.7 % with hrHPV-16 and 7.7 % with hrHPV-18. One case tested positive for both HPV variants (0.9 %). The samples from the anal canal were positive for HPV-16 in 59.8 % of the cases. Simultaneous presence of HPV in the cervix and anal canal was found in 53.8 % of the cases. Regarding expression of E6 RNA, positivity for HPV-16 in the anal canal was found in 21.2 % of the cases, positivity for HPV-16 in the cervix was found in 75.0 %, and positivity for HPV-18 in the cervix was found in 1.9 %. E6 expression in both the cervix and anal canal was found in 19.2 % of the cases. In the controls, 1 % tested positive for HPV-16 and 0 % for HPV-18. Anal samples from the controls showed a hrHPV frequency of 4.9 % (only HPV16). The presence of hrHPV in the anal canal of women with cervical cancer was detected at a high frequency. We also detected E6 RNA expression in the anal canal of women with cervical cancer, suggesting that these women are at risk for anal hrHPV infection.
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Sutton PA, Jones RP, Morrison F, Goldring CE, Park BK, Palmer DH, Malik HZ, Vimalachandran D, Kitteringham NR. Evaluation of a novel tissue stabilization gel to facilitate clinical sampling for translational research in surgical trials. Br J Surg 2015; 102:e124-32. [DOI: 10.1002/bjs.9678] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2014] [Revised: 08/20/2014] [Accepted: 09/19/2014] [Indexed: 12/19/2022]
Abstract
Abstract
Background
The aim was to establish the feasibility of using a tissue stabilization gel (Allprotect™) as an alternative to liquid nitrogen to facilitate collection of clinical samples for translational research.
Methods
Tumour samples from patients undergoing surgery for primary or metastatic colorectal cancer were either snap-frozen in liquid nitrogen or stored in Allprotect™ under a number of different conditions. Sample integrity was compared across different storage conditions by assessing biomolecule stability and function. DNA quality was assessed spectrophotometrically and by KRas genotyping by pyrosequencing. Total RNA retrieval was determined by nanodrop indices/RNA integrity numbers, and quality assessed by reverse transcription–PCR for two representative genes (high-mobility group box 1, HMGB1; carboxylesterase 1, CES1) and two microRNAs (miR122 and let7d). Western blot analysis of HMGB1 and CES1 was used to confirm protein expression, and the metabolic conversion of irinotecan to its active metabolite, SN-38, was used to assess function.
Results
Under short-term storage conditions (up to 1 week) there was no apparent difference in quality between samples stored in Allprotect™ and those snap-frozen in liquid nitrogen. Some RNA degradation became apparent in tissue archived in Allprotect™ after 1 week, and protein degradation after 2 weeks.
Conclusion
In hospitals that do not have access to liquid nitrogen and –80°C freezers, Allprotect™ provides a suitable alternative for the acquisition and stabilization of clinical samples. Storage proved satisfactory for up to 1 week, allowing transfer of samples without the need for specialized facilities. Surgical relevanceAccess to clinical material is a fundamental component of translational research that requires significant infrastructure (research personnel, liquid nitrogen, specialized storage facilities). The aim was to evaluate a new-to-market tissue stabilization gel (Allprotect™), which offers a simple solution to tissue preservation without the need for complex infrastructure.Allprotect™ offers comparable DNA, RNA and protein stabilization to tissue snap-frozen in liquid nitrogen for up to 1 week. Degradation of biomolecules beyond this highlights its role as a short-term tissue preservative.Allprotect™ has the potential to increase surgeon participation in translational research and surgical trials requiring tissue collection.
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Affiliation(s)
- P A Sutton
- Cancer Research UK Centre, UK
- Medical Research Council Centre for Drug Safety Science, University of Liverpool, UK
- Countess of Chester Hospital NHS Foundation Trust, Chester, UK
| | - R P Jones
- Medical Research Council Centre for Drug Safety Science, University of Liverpool, UK
- Liverpool Hepatobiliary Unit, University Hospitals Aintree, Liverpool, UK
| | - F Morrison
- Medical Research Council Centre for Drug Safety Science, University of Liverpool, UK
| | - C E Goldring
- Medical Research Council Centre for Drug Safety Science, University of Liverpool, UK
| | - B K Park
- Medical Research Council Centre for Drug Safety Science, University of Liverpool, UK
| | - D H Palmer
- Cancer Research UK Centre, UK
- Clatterbridge Cancer Centre NHS Foundation Trust, Wirral, UK
| | - H Z Malik
- Liverpool Hepatobiliary Unit, University Hospitals Aintree, Liverpool, UK
| | | | - N R Kitteringham
- Medical Research Council Centre for Drug Safety Science, University of Liverpool, UK
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Yamaguchi T, Mukai H, Yamashita S, Fujii S, Ushijima T. Comprehensive DNA Methylation and Extensive Mutation Analyses of HER2-Positive Breast Cancer. Oncology 2015; 88:377-84. [DOI: 10.1159/000369904] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 11/11/2014] [Indexed: 11/19/2022]
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Abstract
Preanalytic sampling techniques and preparation of tissue specimens strongly influence analytical results in lung tissue diagnostics both on the morphological but also on the molecular level. However, in contrast to analytics where tremendous achievements in the last decade have led to a whole new portfolio of test methods, developments in preanalytics have been minimal. This is specifically unfortunate in lung cancer, where usually only small amounts of tissue are at hand and optimization in all processing steps is mandatory in order to increase the diagnostic yield. In the following, we provide a comprehensive overview on some aspects of preanalytics in lung cancer from the method of sampling over tissue processing to its impact on analytical test results. We specifically discuss the role of preanalytics in novel technologies like next-generation sequencing and in the state-of the-art cytology preparations. In addition, we point out specific problems in preanalytics which hamper further developments in the field of lung tissue diagnostics.
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Affiliation(s)
- Arne Warth
- Institute of Pathology, Heidelberg University, Heidelberg, Germany
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Krishnamurthy S. Biospecimen repositories and cytopathology. Cancer Cytopathol 2014; 123:152-61. [PMID: 25524469 DOI: 10.1002/cncy.21505] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 11/24/2014] [Accepted: 11/24/2014] [Indexed: 12/22/2022]
Abstract
Biospecimen repositories are important for the advancement of biomedical research. Literature on the potential for biobanking of fine-needle aspiration, gynecologic, and nongynecologic cytology specimens is very limited. The potential for biobanking of these specimens as valuable additional resources to surgically excised tissues appears to be excellent. The cervicovaginal specimens that can be used for biobanking include Papanicolaou-stained monolayer preparations and residual material from liquid-based cytology preparations. Different types of specimen preparations of fine-needle aspiration and nongynecologic specimens, including Papanicolaou-stained and Diff-Quik-stained smears, cell blocks. and dedicated passes/residual material from fine-needle aspiration stored frozen in a variety of solutions, can be used for biobanking. Because of several gaps in knowledge regarding the standard of operative procedures for the procurement, storage, and quality assessment of cytology specimens, further studies as well as national conferences and workshops are needed not only to create awareness but also to facilitate the use of cytopathology specimens for biobanking.
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Affiliation(s)
- Savitri Krishnamurthy
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
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Fassbender A, Rahmioglu N, Vitonis AF, Viganò P, Giudice LC, D'Hooghe TM, Hummelshoj L, Adamson GD, Becker CM, Missmer SA, Zondervan KT. World Endometriosis Research Foundation Endometriosis Phenome and Biobanking Harmonisation Project: IV. Tissue collection, processing, and storage in endometriosis research. Fertil Steril 2014; 102:1244-53. [PMID: 25256928 PMCID: PMC4230778 DOI: 10.1016/j.fertnstert.2014.07.1209] [Citation(s) in RCA: 110] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Revised: 07/09/2014] [Accepted: 07/09/2014] [Indexed: 12/13/2022]
Abstract
OBJECTIVE To harmonize standard operating procedures (SOPs) and standardize the recording of associated data for collection, processing, and storage of human tissues relevant to endometriosis. DESIGN An international collaboration involving 34 clinical/academic centers and three industry collaborators from 16 countries on five continents. SETTING In 2013, two workshops were conducted followed by global consultation, bringing together 54 leaders in endometriosis research and sample processing from around the world. PATIENT(S) None. INTERVENTION(S) Consensus SOPs were based on: 1) systematic comparison of SOPs from 24 global centers collecting tissue samples from women with and without endometriosis on a medium or large scale (publication on >100 cases); 2) literature evidence where available, or consultation with laboratory experts otherwise; and 3) several global consultation rounds. MAIN OUTCOME MEASURE(S) Standard recommended and minimum required SOPs for tissue collection, processing, and storage in endometriosis research. RESULT(S) We developed "recommended standard" and "minimum required" SOPs for the collection, processing, and storage of ectopic and eutopic endometrium, peritoneum, and myometrium, and a biospecimen data collection form necessary for interpretation of sample-derived results. CONCLUSION(S) The EPHect SOPs allow endometriosis research centers to decrease variability in tissue-based results, facilitating between-center comparisons and collaborations. The procedures are also relevant to research into other gynecologic conditions involving endometrium, myometrium, and peritoneum. The consensus SOPs are based on the best available evidence; areas with limited evidence are identified as requiring further pilot studies. The SOPs will be reviewed based on investigator feedback and through systematic triannual follow-up. Updated versions will be made available at: http://endometriosisfoundation.org/ephect.
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Affiliation(s)
- Amelie Fassbender
- Organ Systems, Department of Development and Regeneration, KU Leuven, Leuven, Belgium; Department of Obstetrics and Gynecology, Leuven University Fertility Center, University Hospital Leuven, Leuven, Belgium
| | - Nilufer Rahmioglu
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Allison F Vitonis
- Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts; Boston Center for Endometriosis, Boston Children's Hospital and Brigham and Women's Hospital, Boston, Massachusetts
| | - Paola Viganò
- Obstetrics and Gynecology Unit, San Raffaele Scientific Institute, Milano, Italy
| | - Linda C Giudice
- University of California San Francisco, San Francisco, California; World Endometriosis Research Foundation (WERF), London, United Kingdom
| | - Thomas M D'Hooghe
- Organ Systems, Department of Development and Regeneration, KU Leuven, Leuven, Belgium; Department of Obstetrics and Gynecology, Leuven University Fertility Center, University Hospital Leuven, Leuven, Belgium
| | - Lone Hummelshoj
- World Endometriosis Research Foundation (WERF), London, United Kingdom
| | - G David Adamson
- World Endometriosis Research Foundation (WERF), London, United Kingdom; Palo Alto Medical Foundation Fertility Physicians of Northern California, Palo Alto, California
| | - Christian M Becker
- Nuffield Department of Obstetrics and Gynaecology, University of Oxford, Oxford, United Kingdom; Endometriosis Care Centre Oxford, University of Oxford, Oxford, United Kingdom
| | - Stacey A Missmer
- Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts; Boston Center for Endometriosis, Boston Children's Hospital and Brigham and Women's Hospital, Boston, Massachusetts; Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts; Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts
| | - Krina T Zondervan
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom; Nuffield Department of Obstetrics and Gynaecology, University of Oxford, Oxford, United Kingdom; Endometriosis Care Centre Oxford, University of Oxford, Oxford, United Kingdom.
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Evaluation of colon cancer histomorphology: a comparison between formalin and PAXgene tissue fixation by an international ring trial. Virchows Arch 2014; 465:509-19. [DOI: 10.1007/s00428-014-1624-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 06/18/2014] [Accepted: 06/30/2014] [Indexed: 01/15/2023]
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Sato M, Kojima M, Nagatsuma AK, Nakamura Y, Saito N, Ochiai A. Optimal fixation for total preanalytic phase evaluation in pathology laboratories. A comprehensive study including immunohistochemistry, DNA, and mRNA assays. Pathol Int 2014; 64:209-16. [DOI: 10.1111/pin.12164] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Accepted: 04/02/2014] [Indexed: 01/01/2023]
Affiliation(s)
- Masaaki Sato
- Division of Pathology; Research Center for Innovative Oncology; National Cancer Center; Kashiwa Chiba Japan
| | - Motohiro Kojima
- Division of Pathology; Research Center for Innovative Oncology; National Cancer Center; Kashiwa Chiba Japan
| | - Akiko Kawano Nagatsuma
- Division of Pathology; Research Center for Innovative Oncology; National Cancer Center; Kashiwa Chiba Japan
| | - Yuka Nakamura
- Division of Pathology; Research Center for Innovative Oncology; National Cancer Center; Kashiwa Chiba Japan
| | - Norio Saito
- Colorectal and Pelvic Surgery Division; National Cancer Center Hospital East; Kashiwa Chiba Japan
| | - Atsushi Ochiai
- Division of Pathology; Research Center for Innovative Oncology; National Cancer Center; Kashiwa Chiba Japan
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43
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Tissue fixation and the effect of molecular fixatives on downstream staining procedures. Methods 2014; 70:12-9. [PMID: 24561827 PMCID: PMC4240801 DOI: 10.1016/j.ymeth.2014.01.022] [Citation(s) in RCA: 158] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Revised: 01/30/2014] [Accepted: 01/31/2014] [Indexed: 01/11/2023] Open
Abstract
It is impossible to underplay the importance of fixation in histopathology. Whether the scientist is interested in the extraction of information on lipids, proteins, RNA or DNA, fixation is critical to this extraction. This review aims to give a brief overview of the current “state of play” in fixation and focus on the effect fixation, and particularly the effect of the newer brand of “molecular fixatives” have on morphology, histochemistry, immunohistochemistry and RNA/DNA analysis. A methodology incorporating the creation of a fixation tissue microarray for the study of the effect of fixation on histochemistry is detailed.
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44
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Aktas B, Sun H, Yao H, Shi W, Hubbard R, Zhang Y, Jiang T, Ononye SN, Wali VB, Pusztai L, Symmans WF, Hatzis C. Global gene expression changes induced by prolonged cold ischemic stress and preservation method of breast cancer tissue. Mol Oncol 2014; 8:717-27. [PMID: 24602449 DOI: 10.1016/j.molonc.2014.02.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Revised: 01/17/2014] [Accepted: 02/05/2014] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Tissue handling can alter global gene expression potentially affecting the analytical performance of genomic signatures, but such effects have not been systematically evaluated. METHODS Tissue samples from 11 previously untreated breast tumors were minced and aliquots were either snap frozen or placed in RNAlater immediately or after 20, 40, 60, 120 or 180 min at room temperature. RNA was profiled on Affymetrix HG-U133A arrays. We used probe-set-wise hierarchical models to evaluate the effect of preservation method on transcript expression and linear mixed effects models to assess the effect of cold ischemic delay on the expression of individual probe sets. Gene set enrichment analysis identified pathways overrepresented in the affected transcripts. We combined the levels of 41 most sensitive transcripts to develop an index of ischemic stress. RESULTS Concordance in global gene expression between the baseline and 40 min delay was higher for samples preserved in RNAlater (average concordance correlation coefficient CCC = 0.92 compared to 0.88 for snap frozen). Overall, 481 transcripts (3%) were significantly affected by the preservation method, most of them involved in processes important in cancer. Prolonged cold ischemic delay of up to 3 h induced marginal global gene expression changes (average CCC = 0.90 between baseline and 3 h delay). However 41 transcripts were significantly affected by cold ischemic delay. Among the induced transcripts were stress response genes, apoptotic response genes; among the downregulated were genes involved in metabolism, protein processing and cell cycle regulation. An index combining the expression levels of these genes was proportional to the cold ischemic delay. CONCLUSIONS Prolonged cold ischemia induces significant transcriptional changes in a small subset of transcripts in the tissue. Furthermore, the expression level of about 3% of the transcripts is affected by the preservation method. These sensitive transcripts should not be included in genomic signatures for more reliable analytical performance.
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Affiliation(s)
- Bilge Aktas
- Section of Medical Oncology, Yale Cancer Center, Yale School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - Hongxia Sun
- Department of Pathology, UT M.D. Anderson Cancer Center, P.O. Box 85, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - Hui Yao
- Department of Bioinformatics and Computational Biology, UT M.D. Anderson Cancer Center, P.O. Box 301402, Houston, TX 77230, USA
| | - Weiwei Shi
- Section of Medical Oncology, Yale Cancer Center, Yale School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - Rebekah Hubbard
- Department of Pathology, UT M.D. Anderson Cancer Center, P.O. Box 85, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - Ya Zhang
- Department of Pathology, UT M.D. Anderson Cancer Center, P.O. Box 85, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - Tingting Jiang
- Section of Medical Oncology, Yale Cancer Center, Yale School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - Sophia N Ononye
- Section of Medical Oncology, Yale Cancer Center, Yale School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - Vikram B Wali
- Section of Medical Oncology, Yale Cancer Center, Yale School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - Lajos Pusztai
- Section of Medical Oncology, Yale Cancer Center, Yale School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - W Fraser Symmans
- Department of Pathology, UT M.D. Anderson Cancer Center, P.O. Box 85, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - Christos Hatzis
- Section of Medical Oncology, Yale Cancer Center, Yale School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA.
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Molecular fixative enables expression microarray analysis of microdissected clinical cervical specimens. Exp Mol Pathol 2014; 96:168-77. [PMID: 24412268 DOI: 10.1016/j.yexmp.2013.12.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Accepted: 12/06/2013] [Indexed: 11/21/2022]
Abstract
Formalin-fixed tissue has been a mainstay of clinical pathology laboratories, but formalin alters many biomolecules, including nucleic acids and proteins. Meanwhile, frozen tissues contain better-preserved biomolecules, but tissue morphology is affected, limiting their diagnostic utility. Molecular fixatives promise to bridge this gap by simultaneously preserving morphology and biomolecules, enabling clinical diagnosis and molecular analyses on the same specimen. While previous reports have broadly evaluated the use of molecular fixative in various human tissues, we present here the first detailed assessment of the applicability of molecular fixative to both routine histopathological diagnosis and molecular analysis of cervical tissues. Ten specimens excised via the loop electrosurgical excision procedure, which removes conical tissue samples from the cervix, were cut into alternating pieces preserved in either formalin or molecular fixative. Cervical specimens preserved in molecular fixative were easily interpretable, despite featuring more eosinophilic cytoplasm and more recognizable chromatin texture than formalin-fixed specimens. Immunohistochemical staining patterns of p16 and Ki-67 were similar between fixatives, although Ki-67 staining was stronger in the molecular fixative specimens. The RNA of molecular fixative specimens from seven cases representing various dysplasia grades was assessed for utility in expression microarray analysis. Cluster analysis and scatter plots of duplicate samples suggest that data of sufficient quality can be obtained from as little as 50ng of RNA from molecular fixative samples. Taken together, our results show that molecular fixative may be a more versatile substitute for formalin, simultaneously preserving tissue morphology for clinical diagnosis and biomolecules for immunohistochemistry and gene expression analysis.
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46
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Latham GJ. Next-generation sequencing of formalin-fixed, paraffin-embedded tumor biopsies: navigating the perils of old and new technology to advance cancer diagnosis. Expert Rev Mol Diagn 2013; 13:769-72. [PMID: 24117229 DOI: 10.1586/14737159.2013.845090] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Gary J Latham
- Research & Technology Development, Asuragen, Inc., Austin, TX 78744, USA +1 512 681 5272 +1 512 681 5201
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